OK, so that would mean you've used the
apache plugin for authentication as wel as for installing. We can work with that
You should be able to run
certbot --apache again. It should give you the same question again: which hostnames would you like to certify.. Or something like that. It should be possible to select
mail.example.com. Now.. If your certbot is new enough it should ask you if you'd like to expand the current certificate. That means you'll get a single certificate with all the three the hostnames in it.
It's also possible however, it generates a new certificate along side of your previous one. This isn't bad, strictly speaking, but it is very confusing. But nothing we can fix later
So I'd suggest to run the certbot command just again and see what it asks
By the way, opened an issue for the website: https://github.com/certbot/website/issues/660